Interpretive Summary: Peanut is one of the major economically-important legumes that is cultivated worldwide for its’ adaptability to grow in semi-arid environments with relatively low inputs of chemical fertilizers. Due to the limited DNA polymorphisms, the application of marker-assisted breeding in peanut has been impeded. A high density genetic linkage map for all chromosomes is necessary for quantitative trait loci (QTL) analysis and efficient marker-assisted breeding. The objective of this study was to develop a comparative integrated map and to apply in mapping TSWV resistance trait in peanut. A total of 4576 simple sequence repeat (SSR) markers were used for screening polymorphisms. Two markers to differentiate ahFAD2A alleles and ahFAD2B alleles were also included. A total of 324 markers were anchored on this integrated map with 21 linkage groups including 17 aligned to corresponding A-subgenome or B-subgenome (chromosomes A1 to A10, and B1 to B4, B7, B8, and B9). Further, two major TSWV resistance QTLs were identified, which illustrated the application of this map.

Technical Abstract:
Construction and improvement of a genetic map for peanut (Arachis hypogaea L.) continues to be an important task in order to facilitate quantitative trait locus (QTL) analysis and the development of tools for marker-assisted breeding. The objective of this study was to develop a comparative integrated map from two cultivated x cultivated recombinant inbred line (RIL) mapping populations and to apply in mapping TSWV resistance trait in peanut. A total of 4576 simple sequence repeat (SSR) markers from three sources: published SSR markers, newly developed SSR markers from expressed sequence tags (EST) and from bacterial artificial chromosome (BAC) end-sequences were used for screening polymorphisms. Two CAPS (cleaved amplified polymorphic sequence) markers were also included to differentiate ahFAD2A alleles and ahFAD2B alleles. A total of 324 markers were anchored on this integrated map covering 1,352.1 cM with 21 linkage groups (LGs). Combining information from duplicated loci between LGs and comparing with published diploid maps, 7 homoeologous groups were defined and 17 LGs (A1 to A10, B1 to B4, B7, B8, and B9) were aligned to corresponding A-subgenome or B-subgenome of diploid progenitors. One reciprocal translocation was confirmed in the tetraploid cultivated peanut genome. Several chromosomal rearrangements were observed by comparing to published cultivated peanut maps. High consistence with cultivated peanut maps derived from different populations may support this integrated map as a reliable reference map for peanut whole genome sequencing assembling. Further two major QTLs for TSWV resistance were identified for each RILs, which illustrated the application of this map.